1IO4

CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta.

Tahirov, T.H.Inoue-Bungo, T.Morii, H.Fujikawa, A.Sasaki, M.Kimura, K.Shiina, M.Sato, K.Kumasaka, T.Yamamoto, M.Ishii, S.Ogata, K.

(2001) Cell 104: 755-767

  • DOI: https://doi.org/10.1016/s0092-8674(01)00271-9
  • Primary Citation of Related Structures:  
    1HJB, 1HJC, 1IO4

  • PubMed Abstract: 

    The core binding factor (CBF) heterodimeric transcription factors comprised of AML/CBFA/PEBP2alpha/Runx and CBFbeta/PEBP2beta subunits are essential for differentiation of hematopoietic and bone cells, and their mutation is intimately related to the development of acute leukemias and cleidocranial dysplasia. Here, we present the crystal structures of the AML1/Runx-1/CBFalpha(Runt domain)-CBFbeta(core domain)-C/EBPbeta(bZip)-DNA, AML1/Runx-1/CBFalpha(Runt domain)-C/EBPbeta(bZip)-DNA, and AML1/Runx-1/CBFalpha(Runt domain)-DNA complexes. The hydrogen bonding network formed among CBFalpha(Runt domain) and CBFbeta, and CBFalpha(Runt domain) and DNA revealed the allosteric regulation mechanism of CBFalpha(Runt domain)-DNA binding by CBFbeta. The point mutations of CBFalpha related to the aforementioned diseases were also mapped and their effect on DNA binding is discussed.


  • Organizational Affiliation

    Kanagawa Academy of Science and Technology (KAST), Yokohama City University School of Medicine, 3-9 Fukuura, Yokohama 236-0004, Kanazawa-ku, Japan. tahir@med.yokohama-cu.ac.jp


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CAAT/ENHANCER BINDING PROTEIN BETAC [auth A],
D [auth B]
78Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P17676 (Homo sapiens)
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Go to UniProtKB:  P17676
PHAROS:  P17676
GTEx:  ENSG00000172216 
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UniProt GroupP17676
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RUNT-RELATED TRANSCRIPTION FACTOR 1E [auth C]123Mus musculusMutation(s): 0 
UniProt
Find proteins for Q03347 (Mus musculus)
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Go to UniProtKB:  Q03347
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UniProt GroupQ03347
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CORE-BINDING FACTOR, BETA SUBUNITF [auth D]141Mus musculusMutation(s): 0 
UniProt
Find proteins for Q08024 (Mus musculus)
Explore Q08024 
Go to UniProtKB:  Q08024
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UniProt GroupQ08024
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
CSF-1R PROMOTERA [auth E]26N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
CSF-1R PROMOTERB [auth F]26N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.108α = 90
b = 163.6β = 90
c = 109.326γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations